Photoreceptor signaling networks in plant responses to shade

A COP1-PIF-HEC regulatory module fine-tunes photomorphogenesis in Arabidopsis

Light responses mediated by the photoreceptors play crucial roles in regulating different aspects of plant growth and development. An E3 ubiquitin ligase complex CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)1/SUPPRESSOR OF PHYA (SPA), one of the central repressors of photomorphogenesis, is critical for maintaining skotomorphogenesis. It targets several positive regulators of photomorphogenesis for degradation in darkness. Recently, we revealed that basic helix-loop-helix factors, HECATEs (HECs), function as positive regulators of photomorphogenesis by directly interacting and antagonizing the activity of another group of repressors called PHYTOCHROME-INTERACTING FACTORs (PIFs). It was also shown that HECs are partially degraded in the dark through the ubiquitin/26S proteasome pathway. However, the underlying mechanism of HEC degradation in the dark is still unclear. Here, we show that HECs also interact with both COP1 and SPA proteins in darkness, and that HEC2 is directly targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway. Moreover, COP1-mediated polyubiquitylation and degradation of HEC2 are enhanced by PIF1. Therefore, the ubiquitylation and subsequent degradation of HECs are significantly reduced in both cop1 and pif mutants. Consistent with this, the hec mutants partially suppress photomorphogenic phenotypes of both cop1 and pifQ mutants. Collectively, our work reveals that the COP1/SPA-mediated ubiquitylation and degradation of HECs contributes to the coordination of skoto/photomorphogenic development in plants.

ZEITLUPE is required for shade avoidance in the wild tobacco Nicotiana attenuata

Being shaded is a common environmental stress for plants, especially for densely planted crops. Shade decreases red: far-red (R:FR) ratios that inactivate phytochrome B (PHYB) and subsequently release p̱hytochrome i̱nteraction f̱actors (PIFs). Shaded plants display elongated hypocotyls, internodes, and petioles, hyponastic leaves, early flowering and are inhibited in branching: traits collectively called the shade avoidance syndrome (SAS). ZEITLUPE (ZTL) is a circadian clock component and blue light photoreceptor, which is also involved in floral rhythms and plant defense in Nicotiana attenuata. ztl mutants are hypersensitive to red light and ZTL physically interacts with PHYB, suggesting the involvement of ZTL in R:FR light signaling. Here, we show that N. attenuata ZTL-silenced plants display a phenotype opposite to that of the SAS under normal light. After simulated shade, the normally induced transcript levels of the SAS marker gene, ATHB2 are attenuated in ZTL-silenced plants. The auxin signaling pathway, known to be involved in SAS, was also significantly attenuated. Furthermore, NaZTL directly interacts with NaPHYBs, and regulates the transcript levels of PHYBs, PIF3a, PIF7 and PIF8 under shade. Our results suggest that ZTL may regulate PHYB- and the auxin-mediated signaling pathway, which functions in the SAS of N. attenuata.

Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit

The D1 reaction center protein of photosystem II (PSII) is subject to light-induced damage. Degradation of damaged D1 and its replacement by nascent D1 are at the heart of a PSII repair cycle, without which photosynthesis is inhibited. In mature plant chloroplasts, light stimulates the recruitment of ribosomes specifically to psbA mRNA to provide nascent D1 for PSII repair and also triggers a global increase in translation elongation rate. The light-induced signals that initiate these responses are unclear. We present action spectrum and genetic data indicating that the light-induced recruitment of ribosomes to psbA mRNA is triggered by D1 photodamage, whereas the global stimulation of translation elongation is triggered by photosynthetic electron transport. Furthermore, mutants lacking HCF136, which mediates an early step in D1 assembly, exhibit constitutively high psbA ribosome occupancy in the dark and differ in this way from mutants lacking PSII for other reasons. These results, together with the recent elucidation of a thylakoid membrane complex that functions in PSII assembly, PSII repair, and psbA translation, suggest an autoregulatory mechanism in which the light-induced degradation of D1 relieves repressive interactions between D1 and translational activators in the complex. We suggest that the presence of D1 in this complex coordinates D1 synthesis with the need for nascent D1 during both PSII biogenesis and PSII repair in plant chloroplasts.

Artifleck: The Study of Artifactual Responses to Light Flecks with Inappropriate Leaves

Methods in sunfleck research commonly employ the use of experimental leaves which were constructed in homogeneous light. These experimental organs may behave unnaturally when they are challenged with fluctuating light. Photosynthetic responses to heterogeneous light and leaf macronutrient relations were determined for Cycas micronesica, Glycine max, and Zea mays leaves that were grown in homogeneous shade, heterogeneous shade, or full sun. The speed of priming where one light fleck increased the photosynthesis during a subsequent light fleck was greatest for the leaves grown in heterogeneous shade. The rate of induction and the ultimate steady-state photosynthesis were greater for the leaves that were grown in heterogeneous shade versus the leaves grown in homogeneous shade. The leaf mass per area, macronutrient concentration, and macronutrient stoichiometry were also influenced by the shade treatments. The amplitude and direction in which the three developmental light treatments influenced the response variables were not universal among the three model species. The results indicate that the historical practice of using experimental leaves which were constructed under homogeneous light to study leaf responses to fluctuating light may produce artifacts that generate dubious interpretations.

Let it bloom: cross-talk between light and flowering signaling in Arabidopsis

The terrestrial environment is complex, with many parameters fluctuating on daily and seasonal basis. Plants, in particular, have developed complex sensory and signaling networks to extract and integrate information about their surroundings in order to maximize their fitness and mitigate some of the detrimental effects of their sessile lifestyles. Light and temperature each provide crucial insights on the surrounding environment and, in combination, allow plants to appropriately develop, grow and adapt. Cross-talk between light and temperature signaling cascades allows plants to time key developmental decisions to ensure they are 'in sync' with their environment. In this review, we discuss the major players that regulate light and temperature signaling, and the cross-talk between them, in reference to a crucial developmental decision faced by plants: to bloom or not to bloom?

Light Activates Brassinosteroid Biosynthesis to Promote Hook Opening and Petiole Development in Arabidopsis thaliana

Although brassinosteroids (BRs) have been proposed to be negative regulators of photomorphogenesis, their physiological role therein has remained elusive. We studied light-induced photomorphogenic development in the presence of the BR biosynthesis inhibitor, brassinazole (Brz). Hook opening was inhibited in the presence of Brz; this inhibition was reversed in the presence of brassinolide (BL). Hook opening was accompanied by cell expansion on the inner (concave) side of the hook. This cell expansion was inhibited in the presence of Brz but was restored upon the addition of BL. We then evaluated light-induced organ-specific expression of three BR biosynthesis genes, DWF4, BR6ox1 and BR6ox2, and a BR-responsive gene, SAUR-AC1, during the photomorphogenesis of Arabidopsis. Expression of these genes was induced, particularly in the hook region, in response to illumination. The induction peaked after 3 h of light exposure and preceded hook opening. Phytochrome-deficient mutants, hy1, hy2 and phyAphyB, and a light-signaling mutant, hy5, were defective in light-induced expression of BR6ox1, BR6ox2 and SAUR-AC1. Light induced both expression of BR6ox genes and petiole development. Petiole development was inhibited in the presence of Brz. Our results largely contradict the early view that BRs are negative regulators of photomorphogenesis. Our data collectively suggest that light activates the expression of BR biosynthesis genes in the hook region via a phytochrome-signaling pathway and HY5 and that BR biosynthesis is essential for hook opening and petiole development during photomorphogenesis.

Shade avoidance responses become more aggressive in warm environments

When exposed to neighbour cues, competitive plants increase stem growth to reduce the degree of current or future shade. The aim of this work is to investigate the impact of weather conditions on the magnitude of shade avoidance responses in Arabidopsis thaliana. We first generated a growth rate database under controlled conditions and elaborated a model that predicts daytime hypocotyl growth as a function of the activity of the main photosensory receptors (phytochromes A and B, cryptochromes 1 and 2) in combination with light and temperature inputs. We then incorporated the action of thermal amplitude to account for its effect on selected genotypes, which correlates with the dynamics of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR 4. The model predicted growth rate in the field with reasonable accuracy. Thus, we used the model in combination with a worldwide data set of current and future whether conditions. The analysis predicted enhanced shade avoidance responses as a result of higher temperatures due to the geographical location or global warming. Irradiance and thermal amplitude had no effects. These trends were also observed for our local growth rate measurements. We conclude that, if water and nutrients do not become limiting, warm environments enhance the shade avoidance response.

Shade signals alter the expression of circadian clock genes in newly-formed bioenergy sorghum internodes

Stem internodes of bioenergy sorghum inbred R.07020 are longer at high plant density (shade) than at low plant density (control). Initially, the youngest newly-formed subapical stem internodes of shade-treated and control plants are comparable in length. However, full-length internodes of shade-treated plants are three times longer than the internodes of the control plants. To identify the early molecular events associated with internode elongation in response to shade, we analyzed the transcriptome of the newly-formed internodes of shade-treated and control plants sampled between 4 and 6 hr after the start of the light period (14 hr light/10 hr dark). Sorghum genes homologous to the Arabidopsis shade marker genes ATHB2 and PIL1 were not differentially expressed. The results indicate that shade signals promote internode elongation indirectly because sorghum internodes are not illuminated and grow while enclosed with leaf sheaths. Sorghum genes homologous to the Arabidopsis morning-phased circadian clock genes LHY, RVE, and LNK were downregulated and evening-phased genes such as TOC1, PRR5, and GI were upregulated in young internodes in response to shade. We hypothesize that a change in the function or patterns of expression of the circadian clock genes is the earliest molecular event associated with internode elongation in response to shade in bioenergy sorghum. Increased expression of CycD1, which promotes cell division, and decreased expression of cell wall-loosening and MBF1-like genes, which promote cell expansion, suggest that shade signals promote internode elongation in bioenergy sorghum in part through increasing cell number by delaying transition from cell division to cell expansion.

DNA demethylation is involved in the regulation of temperature-dependent anthocyanin accumulation in peach

Anthocyanin biosynthesis is induced by low temperatures in a number of plants. However, in peach (cv Zhonghuashoutao), anthocyanin accumulation was observed in fruit stored at 16°C but not at or below 12°C. Fruit stored at 16°C showed elevated transcript levels of genes encoding anthocyanin biosynthetic enzymes, the transport protein glutathione S-transferase and key transcription factors. Higher transcript levels of PpPAL1/2, PpC4H, Pp4CL4/5/8, PpF3H, PpF3'H, PpDFR1/2/3 and PpANS, as well as transcription factor gene PpbHLH3, were associated with lower methylation levels in the promoter of these genes. The DNA methylation level was further highly correlated with the expression of the DNA methyltransferase genes and DNA demethylase genes. The application of DNA methylation inhibitor 5-azacytidine induced anthocyanin accumulation in peach flesh, further implicating a critical role for DNA demethylation in regulating anthocyanin accumulation in peach flesh. Our data reveal that temperature-dependent DNA demethylation is a key factor to the post-harvest temperature-dependent anthocyanin accumulation in peach flesh.

COP1 destabilizes DELLA proteins in Arabidopsis

DELLA transcriptional regulators are central components in the control of plant growth responses to the environment. This control is considered to be mediated by changes in the metabolism of the hormones gibberellins (GAs), which promote the degradation of DELLAs. However, here we show that warm temperature or shade reduced the stability of a GA-insensitive DELLA allele in Arabidopsis thaliana Furthermore, the degradation of DELLA induced by the warmth preceded changes in GA levels and depended on the E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1). COP1 enhanced the degradation of normal and GA-insensitive DELLA alleles when coexpressed in Nicotiana benthamiana. DELLA proteins physically interacted with COP1 in yeast, mammalian, and plant cells. This interaction was enhanced by the COP1 complex partner SUPRESSOR OF phyA-105 1 (SPA1). The level of ubiquitination of DELLA was enhanced by COP1 and COP1 ubiquitinated DELLA proteins in vitro. We propose that DELLAs are destabilized not only by the canonical GA-dependent pathway but also by COP1 and that this control is relevant for growth responses to shade and warm temperature.

The Photosynthetic Performance of Red Leaf Lettuce under UV-A Irradiation

The objective of this study was to evaluate how different UV-A wavelengths influence the morphology and photosynthetic behavior of red-leaf lettuce (Lactuca sativa L. cv. Maiko). In the experiments, the main photosynthetic photon flux consisted of red (R) and blue (B) light, supplemented with equal doses of different UV-A wavelengths (402, 387 and 367 nm). Treating the crops with low dosages of specific narrow-band UV-A radiation at key points in the life cycle initiated a cascade of responses in the above-ground biomass. According to the results, red-leaf lettuces acclimated to longer UV-A wavelengths by increasing biomass production, whereas different UV-A wavelengths had no significant effect on plant senescence reflectance, nor on the normalized difference vegetation index. A significant decrease in the maximum quantum yield of the PSII photochemistry of dark (Fv/Fm) and light (ΦPSII) adapted plants was observed. A lack of significant changes in non-photochemical fluorescence quenching indicates that photo-inhibition occurred under RBUV367, whereas the photosynthetic response under RB, RBUV402, and RBUV387 suggests that there was no damage to PSII. The correlation of the photosynthetic rate (Pr) with the stomatal conductance (gs) indicated that the increase in the Pr of lettuce under supplemental UV-A radiation was due to the increase of gs, instead of the ratio of the intracellular to ambient CO2 content (Ci/Ca) or stomatal limitations.

Genetic diversity in developmental responses to light spectral quality in barley (Hordeum vulgare L.)

BACKGROUND

Plants use light wavelength, intensity, direction and duration to predict imminent seasonal changes and to determine when to initiate physiological and developmental processes. Among them, crop responses to light are not fully understood. Here, we study how light quality affects barley development, using two broad-spectrum light sources, metal halide (M) and fluorescent (F) lamps. Eleven varieties with known allelic variants for the major flowering time genes were evaluated under controlled conditions (long days, same light intensity). Two experiments were carried out with fully-vernalized plants: 1) control treatments (M, F); 2) shifting chambers 10 days after the start of the experiment (MF, FM).

RESULTS

In general, varieties developed faster under longer exposure to M conditions. The greatest differences were due to a delay promoted by F light bulbs, especially in the time to first node appearance and until the onset of stem elongation. Yield related-traits as the number of seeds were also affected by the conditions experienced. However, not each variety responded equally, and they could be classified in insensitive and sensitive to light quality. Expression levels of flowering time genes HvVRN1, HvFT1 and PPD-H1 were high in M, while HvFT3 and HvVRN2 were higher under F conditions. The expression under shift treatments revealed also a high correlation between HvVRN1 and PPD-H1 transcript levels.

CONCLUSIONS

The characterization of light quality effects has highlighted the important influence of the spectrum on early developmental stages, affecting the moment of onset of stem elongation, and further consequences on the morphology of the plant and yield components. We suggest that light spectra control the vernalization and photoperiod genes probably through the regulation of upstream elements of signalling pathways. The players behind the different responses to light spectra found deserve further research, which could help to optimize breeding strategies.

UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis

Sun-loving plants perceive the proximity of potential light-competing neighboring plants as a reduction in the red:far-red ratio (R:FR), which elicits a suite of responses called the "shade avoidance syndrome" (SAS). Changes in R:FR are primarily perceived by phytochrome B (phyB), whereas UV-B perceived by UV RESISTANCE LOCUS 8 (UVR8) elicits opposing responses to provide a counterbalance to SAS, including reduced shade-induced hypocotyl and petiole elongation. Here we show at the genome-wide level that UVR8 broadly suppresses shade-induced gene expression. A subset of this gene regulation is dependent on the UVR8-stabilized atypical bHLH transcription regulator LONG HYPOCOTYL IN FAR-RED 1 (HFR1), which functions in part redundantly with PHYTOCHROME INTERACTING FACTOR 3-LIKE 1 (PIL1). In parallel, UVR8 signaling decreases protein levels of the key positive regulators of SAS, namely the bHLH transcription factors PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5, in a COP1-dependent but HFR1-independent manner. We propose that UV-B antagonizes SAS via two mechanisms: degradation of PIF4 and PIF5, and HFR1- and PIL1-mediated inhibition of PIF4 and PIF5 function. This work highlights the importance of typical and atypical bHLH transcription regulators for the integration of light signals from different photoreceptors and provides further mechanistic insight into the crosstalk of UVR8 signaling and SAS.

MYCs and PIFs Act Independently in Arabidopsis Growth Regulation

Plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light, collectively called the shade avoidance syndrome (SAS). Plants also have extensive systems to defend themselves against pathogens and herbivores. Defense and shade avoidance are two fundamental components of plant survival and productivity, and there are often tradeoffs between growth and defense. Recently, MYC2, a major positive regulator of defense, was reported to inhibit elongation during shade avoidance. Here, we further investigate the role of MYC2 and the related MYC3 and MYC4 in shade avoidance, and we examine the relationship between MYC2/3/4 and the PIF family of light-regulated transcription factors. We demonstrate that MYC2/3/4 inhibit both elongation and flowering. Furthermore, using both genetic and transcriptomic analysis we find that MYCs and PIFs generally function independently in growth regulation. However, surprisingly, the pif4/5/7 triple mutant restored the petiole shade avoidance response of myc2 (jin1-2) and myc2/3/4 We theorize that increased petiole elongation in myc2/3/4 could be more due to resource tradeoffs or post-translational modifications rather than interactions with PIF4/5/7 affecting gene regulation.

Quantification of Spectral Perception of Plants with Light Absorption of Photoreceptors

Although plant responses to artificial lighting spectra often produce abnormal morphogenesis and reduced productivity, no quantification method to determine how plants perceive and respond to light has been available. Our objective in this study was to test whether a plant's spectral perception can be quantified using the light absorption of its major photoreceptors, phytochrome, cryptochrome, and phototropin. We developed an artificial solar lamp and three different light sources, based on a high-pressure sodium lamp, a fluorescent lamp, and red and blue light-emitting diodes, whose absorption by photoreceptors was equal to that of the standard solar spectrum. Cucumber plants grown under the artificial solar and developed light sources showed normal photomorphogenesis and were indistinguishable from each other. Plants grown under unmodified commercial light sources had abnormal photomorphogenesis that made them short and small. The photosynthetic rate was higher under the unmodified light sources; however, dry masses were highest under the artificial solar and modified light sources, indicating that the cucumber plants are optimized to the solar spectrum. Our results clearly demonstrate that the spectral perceptions of plants can be quantified using the light absorption of their photoreceptors, not visual color or spectra. We expect that our findings will contribute to a better understanding of plant perceptions of and responses to light quality, and improve the productivity of plants cultivated under artificial light.

The JA-pathway MYC transcription factors regulate photomorphogenic responses by targeting HY5 gene expression

Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defence reduces growth are not yet fully understood. Here, we analyze the role of MYC transcription factors (TFs) and jasmonic acid (JA) in photomorphogenic growth. We found that multiple myc mutants share light-associated phenotypes with mutants of the phytochrome B photoreceptor, such as delayed seed germination in the dark and long hypocotyl growth. Overexpression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of red (R) light-regulated genes, including the master regulator HY5. ChIP-seq analyses revealed that MYC2 and MYC3 bind directly to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Altogether, our results pinpoint MYCs as photomorphogenic TFs that control phytochrome responses by activating HY5 expression. This has important implications in understanding the trade-off between growth and defence as the same TFs that activate defence responses are photomorphogenic growth regulators.

Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B

The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.

Shading of the mother plant during seed development promotes subsequent seed germination in soybean

The effect of shading during seed development on subsequent germination remains largely unknown. In this study, two soybean (Glycine max) seed production systems, monocropping (MC) and maize-soybean intercropping (IC), were employed to examine the effects of shading of the mother plant on subsequent seed germination. Compared to the MC soybean seeds, which received light, the developing IC seeds were exposed to shade resulting from the taller neighboring maize plants. The IC seeds germinated faster than the MC seeds, although there was no significant difference in the thickness of the seed coat. The concentration of soluble pro-anthocyanidin in the IC seed coat was significantly lower than that in the MC seed coat. Changes in the concentrations of several types of fatty acids in IC seeds were also observed, the nature of which were consistent with the effect on germination. The expression levels of genes involved in abscisic acid (ABA) biosynthesis were down-regulated in IC seeds, while the transcription levels of the genes related to gibberellin (GA) biosynthesis were up-regulated. This was consistently reflected in decreased ABA concentrations and increased active GA4 concentrations in IC seeds, resulting in an increased GA4/ABA ratio. Our results thus indicated that shading of the mother plant during seed development in soybean promoted subsequent germination by mediating the biosynthesis of pro-anthocyanidins, fatty acids, and phytohormones.

PCH1 and PCHL Directly Interact with PIF1, Promote Its Degradation, and Inhibit Its Transcriptional Function during Photomorphogenesis

PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and PCH1-LIKE (PCHL) were shown to directly bind to phytochrome B (phyB) and suppress phyB thermal reversion, resulting in plants with dramatically enhanced light sensitivity. Here, we show that PCH1 and PCHL also positively regulate various light responses, including seed germination, hypocotyl gravitropism, and chlorophyll biosynthesis, by physically interacting with PHYTOCHROME INTERACTING FACTOR 1 (PIF1) and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). PCH1 and PCHL interact with PIF1 both in the dark and light, and regulate PIF1 abundance. Moreover, PCH1 and PCHL facilitate the physical interaction between phyB and PIF1 in vivo to promote the light-induced degradation of PIF1. PCH1 and PCHL also inhibit the DNA-binding ability of PIF1 to negatively regulate the expressions of PIF1 target genes. In addition, PCH1 and PCHL interact with COP1 and undergo degradation through the 26S proteasome pathway in the dark. Consistently, pch1 suppresses cop1 phenotype in darkness. Collectively, our study reveals a novel mechanism by which PCH1 and PCHL regulate diverse light responses not only by stabilizing phyB Pfr form but also by directly interacting with PIF1 and COP1, providing a molecular understanding of the control of hypocotyl growth by these proteins.

Light Perception: A Matter of Time

Optimizing the perception of external cues and regulating physiology accordingly help plants to cope with the constantly changing environmental conditions to which they are exposed. An array of photoreceptors and intricate signaling pathways allow plants to convey the surrounding light information and synchronize an endogenous timekeeping system known as the circadian clock. This biological clock integrates multiple cues to modulate a myriad of downstream responses, timing them to occur at the best moment of the day and the year. Notably, the mechanism underlying entrainment of the light-mediated clock is not clear. This review addresses known interactions between the light-signaling and circadian-clock networks, focusing on the role of light in clock entrainment and known molecular players in this process.

FHY3 and FAR1 Integrate Light Signals with the miR156-SPL Module-Mediated Aging Pathway to Regulate Arabidopsis Flowering

In response to competition for light from their neighbors, shade-intolerant plants flower precociously to ensure reproductive success and survival. However, the molecular mechanisms underlying this key developmental switch are not well understood. Here, we show that a pair of Arabidopsis transcription factors essential for phytochrome A signaling, FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED IMPAIRED RESPONSE1 (FAR1), regulate flowering time by integrating environmental light signals with the miR156-SPL module-mediated aging pathway. We found that FHY3 and FAR1 directly interact with three flowering-promoting SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, SPL3, SPL4, and SPL5, and inhibit their binding to the promoters of several key flowering regulatory genes, including FRUITFUL (FUL), LEAFY (LFY), APETALA1 (AP1), and MIR172C, thus downregulating their transcript levels and delaying flowering. Under simulated shade conditions, levels of SPL3/4/5 proteins increase, whereas levels of FHY3 and FAR1 proteins decline, thus releasing SPL3/4/5 from FHY3/FAR1 inhibition to allow activation of FUL, LFY, AP1, and MIR172C and, consequently, early flowering. Taken together, these results unravel a novel mechanism whereby plants regulate flowering time by integrating environmental cues (such as light conditions) and an internal developmental program (the miR156-SPL module-mediated aging pathway).

Phytochrome evolution in 3D: deletion, duplication, and diversification

Canonical plant phytochromes are master regulators of photomorphogenesis and the shade avoidance response. They are also part of a widespread superfamily of photoreceptors with diverse spectral and biochemical properties. Plant phytochromes belong to a clade including other phytochromes from glaucophyte, prasinophyte, and streptophyte algae (all members of the Archaeplastida) and those from cryptophyte algae. This is consistent with recent analyses supporting the existence of an AC (Archaeplastida + Cryptista) clade. AC phytochromes have been proposed to arise from ancestral cyanobacterial genes via endosymbiotic gene transfer (EGT), but most recent studies instead support multiple horizontal gene transfer (HGT) events to generate extant eukaryotic phytochromes. In principle, this scenario would be compared to the emerging understanding of early events in eukaryotic evolution to generate a coherent picture. Unfortunately, there is currently a major discrepancy between the evolution of phytochromes and the evolution of eukaryotes; phytochrome evolution is thus not a solved problem. We therefore examine phytochrome evolution in a broader context. Within this context, we can identify three important themes in phytochrome evolution: deletion, duplication, and diversification. These themes drive phytochrome evolution as organisms evolve in response to environmental challenges.

An atypical short-chain dehydrogenase-reductase functions in the relaxation of photoprotective qH in Arabidopsis

Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase-reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PIF proteins

Light-environment signals, sensed by plant phytochrome photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown "trans factors" modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of colocalization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator to regulate the expression of PIF-DTGs through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF-signaling hub.

Plant immunity in signal integration between biotic and abiotic stress responses

Plants constantly monitor and cope with the fluctuating environment while hosting a diversity of plant-inhabiting microbes. The mode and outcome of plant-microbe interactions, including plant disease epidemics, are dynamically and profoundly influenced by abiotic factors, such as light, temperature, water and nutrients. Plants also utilize associations with beneficial microbes during adaptation to adverse conditions. Elucidation of the molecular bases for the plant-microbe-environment interactions is therefore of fundamental importance in the plant sciences. Following advances into individual stress signaling pathways, recent studies are beginning to reveal molecular intersections between biotic and abiotic stress responses and regulatory principles in combined stress responses. We outline mechanisms underlying environmental modulation of plant immunity and emerging roles for immune regulators in abiotic stress tolerance. Furthermore, we discuss how plants coordinate conflicting demands when exposed to combinations of different stresses, with attention to a possible determinant that links initial stress response to broad-spectrum stress tolerance or prioritization of specific stress tolerance.

Cryptochromes integrate green light signals into the circadian system

Plants are acutely sensitive of their light environment, adapting their growth habit and prioritizing developmental decisions to maximize fecundity. In addition to providing an energy source and directional information, light quality also contributes to entrainment of the circadian system, an endogenous timing mechanism that integrates endogenous and environmental signalling cues to promote growth. Whereas plants' perception of red and blue portions of the spectrum are well defined, green light sensitivity remains enigmatic. In this study, we show that low fluence rates of green light are sufficient to entrain and maintain circadian rhythms in Arabidopsis and that cryptochromes contribute to this response. Importantly, green light responses are distinguishable from low blue light-induced phenotypes. These data suggest a distinct signalling mechanism enables entrainment of the circadian system in green light-enriched environments, such as those found in undergrowth and in densely planted monoculture.

Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome

When subject to vegetational shading, shade-avoiding plants detect neighbors by perceiving reduced light quantity and altered light quality. The former includes decreases in the ratio of red to far-red wavelengths (low R:FR) and low blue light ratio (LBL) predominantly detected by phytochromes and cryptochromes, respectively. By integrating multiple signals, plants generate a suite of responses, such as elongation of a variety of organs, accelerated flowering, and reduced branching, which are collectively termed the shade-avoidance syndrome (SAS). To trigger the SAS, interactions between photoreceptors and phytochrome-interacting factors are the general switch for activation of downstream signaling pathways. A number of transcription factor families and phytohormones, especially auxin, gibberellins, ethylene, and brassinosteroids, are involved in the SAS processes. In this review, shade signals, the major photoreceptors involved, and the phenotypic characteristics of the shade-intolerant plant Arabidopsis thaliana are described in detail. In addition, integration of the signaling mechanisms that link photoreceptors with multiple hormone signaling pathways is presented and future research directions are discussed.

Blue and red light affects morphogenesis and 20-hydroxyecdisone content of in vitro Pfaffia glomerata accessions

The combination of different colors from light-emitting diodes (LEDs) may influence growth and production of secondary metabolites in plants. In the present study, the effect of light quality on morphophysiology and content of 20-hydroxyecdysone (20E), a phytoecdysteroid, was evaluated in accessions of an endangered medicinal species, Pfaffia glomerata, grown in vitro. Two accessions (Ac22 and Ac43) were cultured in vitro under three different ratios of red (R) and blue (B) LEDs: (i) 1R:1B, (ii) 1R:3B, and (iii) 3R:1B. An equal ratio of red and blue light (1R:1B) increased biomass accumulation, anthocyanin content, and 20E production (by 30-40%). Moreover, 1R:1B treatment increased the size of vascular bundles and vessel elements, as well as strengthened xylem lignification and thickening of the cell wall of shoots. The 1R:3B treatment induced the highest photosynthetic and electron transport rates and enhanced the activity of oxidative stress-related enzymes. Total Chl content, Chl/Car ratio, and NPQ varied more by accession type than by light source. Spectral quality affected primary metabolism differently in each accession. Specifically, in Ac22 plants, fructose content was higher under 1R:1B and 1R:3B treatments, whereas starch accumulation was higher under 1R:3B, and sucrose under 3R:1B. In Ac43 plants, sugars were not influenced by light spectral quality, but starch content was higher under 3R:1B conditions. In conclusion, red and blue LEDs enhance biomass and 20E production in P. glomerata grown in vitro.

Canopy Light Quality Modulates Stress Responses in Plants

Plants growing at high density are in constant competition for light with each other. The shade avoidance syndrome (SAS) is an effective way to escape neighboring vegetation. Even though the molecular mechanisms regulating SAS have been long studied, interactions between light and other environmental signaling pathways have only recently received attention. Under natural conditions, plants deal with multiple stresses simultaneously. It is, therefore, key to identify commonalities, distinctions, and interactions between plant responses to different environmental cues. This review outlines the current understanding of the interplay between canopy light signaling and other stresses, both biotic and abiotic. Understanding plant responses to multiple stimuli, factoring in the dominance of light for plant life, is essential to generate crops with increased resilience against climate change.

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.

Cell wall structure and composition is affected by light quality in tomato seedlings

Light affects many aspects of cell development. Tomato seedlings growing at different light qualities (white, blue, green, red, far-red) and in the dark displayed alterations in cell wall structure and composition. A strong and negative correlation was found between cell wall thickness and hypocotyl growth. Cell walls was thicker under blue and white lights and thinner under far-red light and in the dark, while intermediate values was observed for red or green lights. Additionally, the inside layer surface of cell wall presented random deposited microfibrillae angles under far-red light and in the dark. However, longitudinal transmission electron microscopy indicates a high frequency of microfibrils close to parallels related to the elongation axis in the outer layer. This was confirmed by ultra-high resolution small angle X-ray scattering. These data suggest that cellulose microfibrils would be passively reoriented in the longitudinal direction. As the cell expands, the most recently deposited layers (inside) behave differentially oriented compared to older (outer) layers in the dark or under FR lights, agreeing with the multinet growth hypothesis. High Ca and pectin levels were found in the cell wall of seedlings growing under blue and white light, also contributing to the low extensibility of the cell wall. Low Ca and pectin contents were found in the dark and under far-red light. Auxins marginally stimulated growth in thin cell wall circumstances. Hypocotyl growth was stimulated by gibberellins under blue light.

Regulation of Photomorphogenic Development by Plant Phytochromes

Photomorphogenesis and skotomorphogenesis are two key events that control plant development, from seed germination to flowering and senescence. A group of wavelength-specific photoreceptors, E3 ubiquitin ligases, and various transcription factors work together to regulate these two critical processes. Phytochromes are the main photoreceptors in plants for perceiving red/far-red light and transducing the light signals to downstream factors that regulate the gene expression network for photomorphogenic development. In this review, we highlight key developmental stages in the life cycle of plants and how phytochromes and other components in the phytochrome signaling pathway play roles in plant growth and development.

UVA Radiation Is Beneficial for Yield and Quality of Indoor Cultivated Lettuce

Understanding the wavelength dependence of plant responses is essential for optimizing production and quality of indoor plant cultivation. UVA is the main component of solar UV radiation, but its role on plant growth is poorly understood. Here, two experiments were conducted to examine whether UVA supplementation is beneficial for indoor plant cultivation. Lettuce (Lactuca sativa L. cv. "Klee") was grown under mixed blue, red, and far-red light with photon flux density of 237 μmol m-2 s-1 in the growth room; photoperiod was 16 h. In the first experiment, three UVA intensities with peak wavelengths at 365 nm were used: 10 (UVA-10), 20 (UVA-20), and 30 (UVA-30) μmol m-2 s-1, respectively. In the second experiment, 10 μmol m-2 s-1 UVA radiation were given for 5 (UVA-5d), 10 (UVA-10d), and 15 (UVA-15d) days before harvest on day 15, respectively. Compared with control (no UVA), shoot dry weight was increased by 27%, 29%, and 15% in the UVA-10, UVA-20, and UVA-30 treatments, respectively, which correlated with 31% (UVA-10), 32% (UVA-20), and 14% (UVA-30) larger leaf area. Shoot dry weight under the treatments of UVA-5d, UVA-10d, and UVA-15d was increased by 18%, 32%, and 30%, respectively, and leaf area was increased by 15%-26%. For both experiments, UVA radiation substantially enhanced secondary metabolites accumulation, e.g. anthocyanin and ascorbic acid contents were increased by 17%-49% and 47%-80%, respectively. Moreover, plants grown under the UVA-30 treatment were stressed, as indicated by lipid peroxidation and lower maximum quantum efficiency of photosystem II photochemistry (Fv/Fm). We conclude that UVA supplementation not only stimulates biomass production in controlled environments, but also enhances secondary metabolite accumulation.

Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors

Phytochrome photoreceptors mediate adaptive responses of plants to red and far-red light. These responses generally entail light-regulated association between phytochromes and other proteins, among them the phytochrome-interacting factors (PIF). The interaction with Arabidopsis thaliana phytochrome B (AtPhyB) localizes to the bipartite APB motif of the A. thaliana PIFs (AtPIF). To address a dearth of quantitative interaction data, we construct and analyze numerous AtPIF3/6 variants. Red-light-activated binding is predominantly mediated by the APB N-terminus, whereas the C-terminus modulates binding and underlies the differential affinity of AtPIF3 and AtPIF6. We identify AtPIF variants of reduced size, monomeric or homodimeric state, and with AtPhyB affinities between 10 and 700 nM. Optogenetically deployed in mammalian cells, the AtPIF variants drive light-regulated gene expression and membrane recruitment, in certain cases reducing basal activity and enhancing regulatory response. Moreover, our results provide hitherto unavailable quantitative insight into the AtPhyB:AtPIF interaction underpinning vital light-dependent responses in plants.

David Golonka et al. report the epitopes in Arabidopsis phytochrome-interacting factors (PIF) that underlie light-dependent interactions with phytochrome B. They identify compact PIF variants that enable light-activated gene expression and membrane recruitment with reduced basal activity and enhanced regulatory response.

Slow induction of chlorophyll a fluorescence excited by blue and red light in Tradescantia leaves acclimated to high and low light

Tradescantia is a good model for assaying induction events in higher plant leaves. Chlorophyll (Chl) fluorescence serves as a sensitive reporter of the functional state of photosynthetic apparatus in chloroplasts. The fluorescence time-course depends on the leaf growth conditions and actinic light quality. In this work, we investigated slow induction of Chl a fluorescence (SIF) excited by blue light (BL, λ_max = 455 nm) or red light (RL, λ_max = 630 nm) in dark-adapted leaves of Tradescantia fluminensis acclimated to high light (~ 1000 µmol photons m^-2 s^-1; HL) or low light (~ 100 µmol photons m^-2 s^-1; LL). Our special interest was focused on the contribution of the avoidance response to SIF kinetics. Bearing in mind that BL and RL have different impacts on photoreceptors that initiate chloroplast movements within the cell (accumulation/avoidance responses), we have compared the SIF patterns during the action of BL and RL. The time-courses of SIF and kinetics of non-photochemical quenching (NPQ) of Chl a fluorescence revealed a certain difference when leaves were illuminated by BL or RL. In both cases, the yield of fluorescence rose to the maximal level P and then, after the lag-phase P-S-M₁, the fluorescence level decreased toward the steady state T (via the intermediate phases M₁-M₂ and M₂-T). In LL-acclimated leaves, the duration of the P-S-M₁ phase was almost two times longer that in HL-grown plants. In the case of BL, the fluorescence decay included the transient phase M₁-M₂. This phase was obscure during the RL illumination. Non-photochemical quenching of Chl a fluorescence has been quantified as [Formula: see text], where [Formula: see text] and [Formula: see text] stand for the fluorescence response to saturating pulses of light applied to dark-adapted and illuminated samples, respectively. The time-courses of such a formally determined NPQ value were markedly different during the action of RL and BL. In LL-grown leaves, BL induced higher NPQ as compared to the action of RL. In HL-grown plants, the difference between the NPQ responses to BL and RL illumination was insignificant. Comparing the peculiarities of Chl a fluorescence induced by BL and RL, we conclude that the avoidance response can provide a marked contribution to SIF and NPQ generation. The dependence of NPQ on the quality of actinic light suggests that chloroplast movements within the cell have a noticeable impact on the formally determined NPQ value. Analyzing kinetics of post-illumination decay of NPQ in the context of solar stress resistance, we have found that LL-acclimated Tradescantia leaves are more vulnerable to strong light than the HL-grown leaves.

FAR-RED ELONGATED HYPOCOTYLS3 negatively regulates shade avoidance responses in Arabidopsis

Light is a key limiting factor of plant growth and development under the canopy. Specific light signals, such as a low ratio of red : far-red (R:FR) light, trigger the shade avoidance response, which affects hypocotyl, stem, and leaf growth. Although multiple components mediating shade avoidance responses have been identified in the past few decades, the underlying regulatory mechanism remains unclear. In this study, we found that the far-red elongated hypocotyls 3 (fhy3) mutant exhibited longer hypocotyls and increased expression levels of core shade avoidance response genes under low R:FR shade conditions compared with the wild type No-0, suggesting that FHY3 negatively regulates shade avoidance responses. Yeast one-hybrid, chromatin immunoprecipitation, and RT-qPCR assays revealed that FHY3 directly binds to the promoters and gene body of PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2 and activates their expression to inhibit shade responses. Furthermore, the overexpression of PAR1 or PAR2 rescued the enhanced shade avoidance responses of fhy3, indicating that both genes are direct downstream targets of FHY3 that mediate shade avoidance responses. Our findings demonstrate that the light-signalling protein FHY3 positively regulates the transcription of PAR1 and PAR2, which encode two key negative regulators of shade avoidance responses, thus repressing plant responses to shade signals.

Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants

Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome

Background

Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts.

Results

In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing.

Conclusions

This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.

Source Strength Modulates Fruit Set by Starch Turnover and Export of Both Sucrose and Amino Acids in Pepper

Fruit set is an important yield-related parameter, which varies drastically due to genetic and environmental factors. Here, two commercial cultivars of Capsicum chinense (Biquinho and Habanero) were evaluated in response to light intensity (unshaded and shaded) and N supply (deficiency and sufficiency) to understand the role of source strength on fruit set at the metabolic level. We assessed the metabolic balance of primary metabolites in source leaves during the flowering period. Furthermore, we investigated the metabolic balance of the same metabolites in flowers to gain more insights into their influence on fruit set. Genotype and N supply had a strong effect on fruit set and the levels of primary metabolites, whereas light intensity had a moderate effect. Higher fruit set was mainly related to the export of both sucrose and amino acids from source leaves to flowers. Additionally, starch turnover in source leaves, but not in flowers, had a central role on the sucrose supply to sink organs at night. In flowers, our results not only confirmed the role of the daily supply of carbohydrates on fruit set but also indicated a potential role of the balance of amino acids and malate.

Coincidence of potato CONSTANS (StCOL1) expression and light cannot explain night-break repression of tuberization

In the obligate short-day potato Solanum tuberosum group Andigena (Solanum andigena), short days, or actually long nights, induce tuberization. Applying a night break in the middle of this long night represses tuberization. However, it is not yet understood how this repression takes place. We suggest a coincidence model, similar to the model explaining photoperiodic flowering in Arabidopsis. We hypothesize that potato CONSTANS (StCOL1), expressed in the night of a short day, is stabilized by the light of the night break. This allows for StCOL1 to repress tuberization through induction of StSP5G, which represses the tuberization signal StSP6A. We grew S. andigena plants in short days, with night breaks applied at different time points during the dark period, either coinciding with StCOL1 expression or not. StCOL1 protein presence, StCOL1 expression and expression of downstream targets StSP5G and StSP6A were measured during a 24-h time course. Our results show that a night break applied during peak StCOL1 expression is unable to delay tuberization, while coincidence with low or no StCOL1 expression leads to severely repressed tuberization. These results imply that coincidence between StCOL1 expression and light does not explain why a night break represses tuberization in short days. Furthermore, stable StCOL1 did not always induce StSP5G, and upregulated StSP5G did not always lead to fully repressed StSP6A. Our findings suggest there is a yet unknown level of control between StCOL1, StSP5G and StSP6A expression, which determines whether a plant tuberizes.

Identification and functional analysis of proteins in response to light intensity, temperature and water potential in Brassica rapa hypocotyl

Hypocotyl elongation is an early event in plant growth and development and is sensitive to fluctuations in light, temperature, water potential and nutrients. Most research on hypocotyl elongation has focused on the regulatory mechanism of a single environment factor. However, information about combined effects of multi-environment factors remains unavailable, and overlapping sites of the environmental factors signaling pathways in the regulation of hypocotyl elongation remain unclear. To identify how cross-talks among light intensity, temperature and water potential regulate hypocotyl elongation in Brassica rapa L. ssp. chinesis, a comprehensive isobaric tag for relative and absolute quantitation-based proteomic approach was adopted. In total, 7259 proteins were quantified, and 378 differentially expressed proteins (DEPs) were responsive to all three environmental factors. The DEPs were involved in a variety of biochemical processes, including signal transduction, cytoskeletal organization, carbohydrate metabolism, cell wall organization, protein modification and transport. The DEPs did not function in isolation, but acted in a large and complex interaction network to affect hypocotyl elongation. Among the DEPs, phyB was outstanding for its significant fold change in quantity and complex interaction networks with other proteins. In addition, changes of sensitivity to environmental factors in phyB-9 suggested a key role in the regulation of hypocotyl elongation. Overall, the data presented in this study show a profile of proteins interaction network in response to light intensity, temperature and water potential and provides molecular basis of hypocotyl elongation in B. rapa.

Neighbour signals perceived by phytochrome B increase thermotolerance in Arabidopsis

Due to the preeminence of reductionist approaches, understanding of plant responses to combined stresses is limited. We speculated that light-quality signals of neighbouring vegetation might increase susceptibility to heat shocks because shade reduces tissue temperature and hence the likeness of heat shocks. In contrast, plants of Arabidopsis thaliana grown under low-red/far-red ratios typical of shade were less damaged by heat stress than plants grown under simulated sunlight. Neighbour signals reduce the activity of phytochrome B (phyB), increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs). The phyB mutant showed high tolerance to heat stress even under simulated sunlight, and a pif multiple mutant showed low tolerance under simulated shade. phyB and red/far-red ratio had no effects on seedlings acclimated with nonstressful warm temperatures before the heat shock. The phyB mutant showed reduced expression of several fatty acid desaturase (FAD) genes and less proportion of fully unsaturated fatty acids and electrolyte leakage of membranes exposed to heat shocks. Red-light-activated phyB also reduced thermotolerance of dark-grown seedlings but not via changes in FADs expression and membrane stability. We propose that the reduced photosynthetic capacity linked to thermotolerant membranes would be less costly under shade, where the light input limits photosynthesis.

System Analysis of MIRNAs in Maize Internode Elongation

MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.

Identification of TCP13 as an Upstream Regulator of ATHB12 during Leaf Development

Leaves grow by distinct phases controlled by gene regulatory networks including many transcription factors. Arabidopsis thaliana homeobox 12 (ATHB12) promotes leaf growth especially during the cell expansion phase. In this study, we identify TCP13, a member of the TCP transcription factor family, as an upstream inhibitor of ATHB12. Yeast one-hybrid screening using a 1.2-kb upstream region of ATHB12 resulted in the isolation of TCP13 as well as other transcription factors. Transgenic plants constitutively expressing TCP13 displays a significant reduction in leaf cell size especially during the cell expansion period, while repression of TCP13 and its paralogs (TCP5 and TCP17) result in enlarged leaf cells, indicating that TCP13 and its paralogs inhibit leaf development, mainly at the cell expansion phase. Its expression pattern during leaf expansion phase is opposite to ATHB12 expression. Consistently, the expression of ATHB12 and its downstream genes decreases when TCP13 was overexpressed, and increases when the expression of TCP13 and its paralogs is repressed. In chromatin immunoprecipitation assays using TCP13-GFP plants, a fragment of the ATHB12 upstream region that contains the consensus sequence for TCP binding is strongly enriched. Taken together, these findings indicate that TCP13 and its paralogs inhibit leaf growth by repressing ATHB12 expression.

A meta-analysis of plant responses to light intensity for 70 traits ranging from molecules to whole plant performance

By means of meta-analyses we determined how 70 traits related to plant anatomy, morphology, chemistry, physiology, growth and reproduction are affected by daily light integral (DLI; mol photons m^-2  d^-1 ). A large database including 500 experiments with 760 plant species enabled us to determine generalized dose-response curves. Many traits increase with DLI in a saturating fashion. Some showed a more than 10-fold increase over the DLI range of 1-50 mol m^-2  d^-1 , such as the number of seeds produced per plant and the actual rate of photosynthesis. Strong decreases with DLI (up to three-fold) were observed for leaf area ratio and leaf payback time. Plasticity differences among species groups were generally small compared with the overall responses to DLI. However, for a number of traits, including photosynthetic capacity and realized growth, we found woody and shade-tolerant species to have lower plasticity. We further conclude that the direction and degree of trait changes adheres with responses to plant density and to vertical light gradients within plant canopies. This synthesis provides a strong quantitative basis for understanding plant acclimation to light, from molecular to whole plant responses, but also identifies the variables that currently form weak spots in our knowledge, such as respiration and reproductive characteristics.

Regulation of Alternative Splicing by Phytochrome

Recently, phytochrome has been shown to regulate not only transcription but also alternative splicing at a similar genomic scale in Arabidopsis. Here I describe the protocols for detecting phytochrome-mediated light-responsive alterations in alternative splicing in Arabidopsis, using RT-PCR technique followed by quantification with the Bioanalyzer.

A perspective on ecologically relevant plant-UV research and its practical application

Plants perceive ultraviolet-B (UV-B) radiation through the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8), and initiate regulatory responses via associated signalling networks, gene expression and metabolic pathways. Various regulatory adaptations to UV-B radiation enable plants to harvest information about fluctuations in UV-B irradiance and spectral composition in natural environments, and to defend themselves against UV-B exposure. Given that UVR8 is present across plant organs and tissues, knowledge of the systemic signalling involved in its activation and function throughout the plant is important for understanding the context of specific responses. Fine-scale understanding of both UV-B irradiance and perception within tissues and cells requires improved application of knowledge about UV-attenuation in leaves and canopies, warranting greater consideration when designing experiments. In this context, reciprocal crosstalk among photoreceptor-induced pathways also needs to be considered, as this appears to produce particularly complex patterns of physiological and morphological response. Through crosstalk, plant responses to UV-B radiation go beyond simply UV-protection or amelioration of damage, but may give cross-protection over a suite of environmental stressors. Overall, there is emerging knowledge showing how information captured by UVR8 is used to regulate molecular and physiological processes, although understanding of upscaling to higher levels of organisation, i.e. organisms, canopies and communities remains poor. Achieving this will require further studies using model plant species beyond Arabidopsis, and that represent a broad range of functional types. More attention should also be given to plants in natural environments in all their complexity, as such studies are needed to acquire an improved understanding of the impact of climate change in the context of plant-UV responses. Furthermore, broadening the scope of experiments into the regulation of plant-UV responses will facilitate the application of UV radiation in commercial plant production. By considering the progress made in plant-UV research, this perspective highlights prescient topics in plant-UV photobiology where future research efforts can profitably be focussed. This perspective also emphasises burgeoning interdisciplinary links that will assist in understanding of UV-B effects across organisational scales and gaps in knowledge that need to be filled so as to achieve an integrated vision of plant responses to UV-radiation.

Orthogonal regulation of phytochrome B abundance by stress-specific plastidial retrograde signaling metabolite

Plant survival necessitates constant monitoring of fluctuating light and balancing growth demands with adaptive responses, tasks mediated via interconnected sensing and signaling networks. Photoreceptor phytochrome B (phyB) and plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) are evolutionarily conserved sensing and signaling components eliciting responses through unknown connection(s). Here, via a suppressor screen, we identify two phyB mutant alleles that revert the dwarf and high salicylic acid phenotypes of the high MEcPP containing mutant ceh1. Biochemical analyses show high phyB protein levels in MEcPP-accumulating plants resulting from reduced expression of phyB antagonists and decreased auxin levels. We show that auxin treatment negatively regulates phyB abundance. Additional studies identify CAMTA3, a MEcPP-activated calcium-dependent transcriptional regulator, as critical for maintaining phyB abundance. These studies provide insights into biological organization fundamentals whereby a signal from a single plastidial metabolite is transduced into an ensemble of regulatory networks controlling the abundance of phyB, positioning plastids at the information apex directing adaptive responses.

MEcPP is an evolutionarily conserved metabolite that acts as a plastid-to-nucleus retrograde signal to regulate adaptive responses to fluctuating light. Here the authors show that MEcPP regulates seedling development by stabilizing the phyB photoreceptor in an auxin and Ca²⁺ dependent manner.

Shade delays flowering in Medicago sativa

Shade-intolerant plants respond to the decrease in the red (R) to far-red (FR) light ratio (R:FR) occurring under shade by elongating stems and petioles and by re-positioning leaves, in a race to outcompete neighbors for the sunlight resource. In some annual species, the shade avoidance syndrome (SAS) is accompanied by the early induction of flowering. Anticipated flowering is viewed as a strategy to set seeds before the resources become severely limiting. Little is known about the molecular mechanisms of SAS in perennial forage crops like alfalfa (Medicago sativa). To study SAS in alfalfa, we exposed alfalfa plants to simulated shade by supplementing with FR light. Low R:FR light produced a classical SAS, with increased internode and petiole lengths, but unexpectedly also with delayed flowering. To understand the molecular mechanisms involved in uncoupling SAS from early flowering, we used a transcriptomic approach. The SAS is likely to be mediated by increased expression of msPIF3 and msHB2 in low R:FR light. Constitutive expression of these genes in Arabidopsis led to SAS, including early flowering, strongly suggesting that their roles are conserved. Delayed flowering was likely to be mediated by the downregulation of msSPL3, which promotes flowering in both Arabidopsis and alfalfa. Shade-delayed flowering in alfalfa may be important to extend the vegetative phase under suboptimal light conditions, and thus assure the accumulation of reserves necessary to resume growth after the next season.